Rumen Microbiota, Predicted Metabolic Pathways, and Fermentation Parameters Exhibit Production-System-Specific Associations in Cattle and Goats

The specific differences, unique characteristics, and functional linkages of rumen microbiota and their metabolic pathways across different ruminant species remain poorly understood. To investigate these cross-species relationships, 16 Holstein cows, 28 Simmental crossbred cattle, and 15 Boer goats were fed under standardized conditions for 97 days. Rumen microbial composition and function were evaluated using 16S rRNA gene sequencing and PICRUSt. Results revealed distinct, host-specific microbial architectures. Holstein cows exhibited an overall enrichment of the phylum Proteobacteria and ABC transporter pathways. Notably, their micro-ecosystem was dominated by the Succinivibrionaceae_UCG-001 flora type, which is computationally associated with propionate synthesis for milk production and is predicted to potentially contribute to altered methane metabolism. In contrast, Simmental cattle were characterized by Succinivibrionaceae_UCG-002 and computationally upregulated glycolysis/gluconeogenesis pathways, which are associated with volatile fatty acid conversion for energy deposition. Furthermore, Boer goats harbored a unique fiber-adapted ecosystem exclusively enriched with the norank_f_Bacteroidales_BS11_gut_group and Lachnospiraceae_ND3007_group, correlating with butyrate production and maintaining a classic acetate-type fermentation profile, while exhibiting an elevated predicted genomic potential for methane production based on functional profiling. This study demonstrates that rumen microbiota, metabolic pathways, and fermentation parameters form a highly coordinated network shaped by host phylogeny, energy allocation, and specific diets, providing a theoretical basis for targeted microbiome modifications to improve animal health and feed utilization.